Quantum algorithm for alchemical optimization in material design

The development of tailored materials for specific applications is an active field of research in chemistry, material science and drug discovery. The number of possible molecules obtainable from a set of atomic species grow exponentially with the size of the system, limiting the efficiency of classical sampling algorithms. On the other hand, quantum computers can provide an efficient solution to the sampling of the chemical compound space for the optimization of a given molecular property. In this work, we propose a quantum algorithm for addressing the material design problem with a favourable scaling. The core of this approach is the representation of the space of candidate structures as a linear superposition of all possible atomic compositions. The corresponding ‘alchemical’ Hamiltonian drives the optimization in both the atomic and electronic spaces leading to the selection of the best fitting molecule, which optimizes a given property of the system, e.g., the interaction with an external potential as in drug design. The quantum advantage resides in the efficient calculation of the electronic structure properties together with the sampling of the exponentially large chemical compound space. We demonstrate both in simulations and with IBM Quantum hardware the efficiency of our scheme and highlight the results in a few test cases. This preliminary study can serve as a basis for the development of further material design quantum algorithms for near-term quantum computers.

‘Alchemical’ quantum algorithm for the simultaneous optimisation of chemical composition and electronic structure for material design. By exploiting quantum mechanical principles this approach will boost drug discovery in the near future.     

Influence of the Degree of Deacetylation of Chitosan and BMP-2 Concentration on Biocompatibility and Osteogenic Properties of BMP-2/PLA Granule-Loaded Chitosan/β-Glycerophosphate Hydrogels

Compositions based on chitosan/β-glycerophosphate hydrogels with highly porous polylactide granules can be used to obtain moldable bone graft materials that have osteoinductive and osteoconductive properties. To eliminate the influence of such characteristics as chain length, degree of purification, and molecular weight on a designed material, the one-stock chitosan sample was reacetylated to degrees of deacetylation (DD%) of 19.5, 39, 49, 55, and 56. A study of the chitosan/β-glycerophosphate hydrogel with chitosan of a reduced DD% showed that a low degree of deacetylation increased the MSCs (multipotent stromal cells) viability rate in vitro and reduced the leukocyte infiltration in subcutaneous implantation to Wistar rats in vivo. The addition of 12 wt% polylactide granules resulted in optimal composite mechanical and moldable properties, and increased the modulus of elasticity of the hydrogel-based material by approximately 100 times. Excessive filling of the material with PLA (polylactide) granules (more than 20%) led to material destruction at a ~10% strain. Osteoinductive and osteoconductive properties of the chitosan hydrogel-based material with reacetylated chitosan (39 DD%) and highly porous polylactide granules impregnated with BMP-2 (bone morphogenetic protein-2) have been demonstrated in models of orthotopic and ectopic bone formation. When implanted into a critical-size calvarial defect in rats, the optimal concentration of BMP-2 was 10 μg/mL: bone tissue areas filled the entire material’s thickness. Implantation of the material with 50 μg/mL BMP-2 was accompanied with excessive growth of bone tissue and material displacement beyond the defect. Significant osteoinductive and osteoconductive properties of the material with 10 μg/mL of BMP-2 were also shown in subcutaneous implantation.     

Application of Octanohydroxamic Acid for Salting out Liquid–Liquid Extraction of Materials for Energy Storage in Supercapacitors

The ability to achieve high areal capacitance for oxide-based supercapacitor electrodes with high active mass loadings is critical for practical applications. This paper reports the feasibility of the fabrication of Mn₃O₄-multiwalled carbon nanotube (MWCNT) composites by the new salting-out method, which allows direct particle transfer from an aqueous synthesis medium to a 2-propanol suspension for the fabrication of advanced Mn₃O₄-MWCNT electrodes for supercapacitors. The electrodes show enhanced capacitive performance at high active mass loading due to reduced particle agglomeration and enhanced mixing of the Mn₃O₄ particles and conductive MWCNT additives. The strategy is based on the multifunctional properties of octanohydroxamic acid, which is used as a capping and dispersing agent for Mn₃O₄ synthesis and an extractor for particle transfer to the electrode processing medium. Electrochemical studies show that high areal capacitance is achieved at low electrode resistance. The electrodes with an active mass of 40.1 mg cm⁻² show a capacitance of 4.3 F cm⁻² at a scan rate of 2 mV s⁻¹. Electron microscopy studies reveal changes in electrode microstructure during charge-discharge cycling, which can explain the increase in capacitance. The salting-out method is promising for the development of advanced nanocomposites for energy storage in supercapacitors.     

Point Mutations of Nicotinic Receptor α1 Subunit Reveal New Molecular Features of G153S Slow-Channel Myasthenia

Slow-channel congenital myasthenic syndromes (SCCMSs) are rare genetic diseases caused by mutations in muscle nicotinic acetylcholine receptor (nAChR) subunits. Most of the known SCCMS-associated mutations localize at the transmembrane region near the ion pore. Only two SCCMS point mutations are at the extracellular domains near the acetylcholine binding site, α1(G153S) being one of them. In this work, a combination of molecular dynamics, targeted mutagenesis, fluorescent Ca²⁺ imaging and patch-clamp electrophysiology has been applied to G153S mutant muscle nAChR to investigate the role of hydrogen bonds formed by Ser 153 with C-loop residues near the acetylcholine-binding site. Introduction of L199T mutation to the C-loop in the vicinity of Ser 153 changed hydrogen bonds distribution, decreased acetylcholine potency (EC₅₀ 2607 vs. 146 nM) of the double mutant and decay kinetics of acetylcholine-evoked cytoplasmic Ca²⁺ rise (τ 14.2 ± 0.3 vs. 34.0 ± 0.4 s). These results shed light on molecular mechanisms of nAChR activation-desensitization and on the involvement of such mechanisms in channelopathy genesis.     

Monitoring and Statistical Analysis of Formation of Organochlorine and Organobromine Compounds in Drinking Water of Different Water Intakes

The main drawback of drinking water chlorination involves the formation of quite hazardous disinfection by-products (DBPs), represented mainly by halogenated species. Based on the authors’ monitoring data since 2002, the prevalence of chlorine over bromine in the composition of volatile DBPs was shown for the drinking water in Ufa (Russia). However, the situation was completely reversed in the case of semi-volatile DBPs. The principal goal of the present study involved rationalization of the results of the long-term monitoring. Gas chromatography–mass spectrometry (GC-MS) was used for the qualitative and quantitative analysis of volatile DBPs. Identification of semi-volatile compounds was carried out with GC-MS, while gas chromatography with an atomic emission detector (GC-AED) was used for their quantification. A significant contribution of oxygen to the composition of semi-volatile compounds proves the decisive role of the dissolved organic matter oxidative destructive processes. Statistical analysis revealed notable linear correlations for trihalomethane and haloacetic acid formation vs. chlorine dose. On the contrary, halogenated semi-volatile products do not demonstrate any correlations with the water quality parameters or chlorine dose. Principal component analysis (PCA) placed them into separate groups. The results allow for proposing that formation of the organohalogenated species involved the fast penetration of bromine into the humic matter molecules and, further, their oxidative destruction by active chlorine.     

Size and Structure of Empty and Filled Nanocontainer Based on Peptide Dendrimer with Histidine Spacers at Different pH

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines.     

Generation of a Hetero Spin Complex from Iron(II) Iodide with Redox Active Acenaphthene-1,2-Diimine

The reaction of the redox active 1,2-bis[(2,6-diisopropylphenyl)imino]acenaphthene (dpp-BIAN) and iron(II) iodide in acetonitrile led to a new complex [(dpp-BIAN)Fe^III₂] (1). Molecular structure of 1 was determined by the single crystal X-ray diffraction analysis. The spin state of the iron cation in complex 1 at room temperature and the magnetic behavior of 1 in the temperature range of 2–300 K were studied using Mossbauer spectroscopy and magnetic susceptibility measurements, respectively. The neutral character of dpp-BIAN in 1 was confirmed by IR and UV spectroscopy. The electrochemistry of 1 was studied in solution and solid state using cyclic voltammetry. The generation of the radical anion form of the dpp-BIAN ligand upon reduction of 1 in a CH₂Cl₂ solution was monitored by EPR spectroscopy.     

Novel c-Jun N-Terminal Kinase (JNK) Inhibitors with an 11H-Indeno[1,2-b]quinoxalin-11-one Scaffold

c-Jun N-terminal kinase (JNK) plays a central role in stress signaling pathways implicated in important pathological processes, including rheumatoid arthritis and ischemia-reperfusion injury. Therefore, inhibition of JNK is of interest for molecular targeted therapy to treat various diseases. We synthesized 13 derivatives of our reported JNK inhibitor 11H-indeno[1,2-b]quinoxalin-11-one oxime and evaluated their binding to the three JNK isoforms and their biological effects. Eight compounds exhibited submicromolar binding affinity for at least one JNK isoform. Most of these compounds also inhibited lipopolysaccharide (LPS)-induced nuclear factor-κB/activating protein 1 (NF-κB/AP-1) activation and interleukin-6 (IL-6) production in human monocytic THP1-Blue cells and human MonoMac-6 cells, respectively. Selected compounds (4f and 4m) also inhibited LPS-induced c-Jun phosphorylation in MonoMac-6 cells, directly confirming JNK inhibition. We conclude that indenoquinoxaline-based oximes can serve as specific small-molecule modulators for mechanistic studies of JNKs, as well as potential leads for the development of anti-inflammatory drugs.     

2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides: synthesis,stereospecificity, some chemical transformations,and conformational analysis

The synthesis of methyl 5-O-benzoyl-2-chloro-2,3-dideoxy-3-fluoro-beta-d-ribofuranoside (5) and its use as a glycosylating agent for persilylated thymine, N(6)-benzoyladenine, and N(4)-benzoylcytosine are described (Scheme 1). The 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides 10-12 synthesized were transformed to 2',3'-dideoxy-3'-fluoro-alpha- and -beta-d-erythro-pentofuranoside nucleosides of thymine (13a,b), adenine (14a,b), and cytidine (15a,b) by treatment with tributyltin hydride in the presence of alpha,alpha'-azobisisobutyronitrile (Scheme 2). Treatment of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides with 1 M MeONa/MeOH under reflux for 1-5 h afforded 2',3'-didehydro-2',3'-dideoxy-2'-chloro-d-pentofuranosyl nucleosides as the principal products (47-81%) of the reaction, along with recovered starting nucleoside (11-33%) (Scheme 3). Easy HF elimination was also observed in the case of the 2'-azido-2',3'-dideoxy-3'-fluoro-beta-d-ribofuranosides of thymine (17) and adenine (20) (Scheme 3). The role of conformational peculiarities of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides as well as of 17 and 20 in the observed exclusive elimination of HF is discussed. The conformational analysis of a rather broad palette of 2,3-dideoxy-3-fluoro-2-(X-substituted)-d-ribofuranosides was performed with the aid of the PSEUROT (version 6.3) program, using (i) the recently reparametrized Karplus-type relation (Chattopadhyaya and co-workers. J. Org. Chem. 1998, 63, 4967) and (ii) empirical bond angle correction terms suggested by us. The predictive power of the Brunck and Weinhold model (J. Am. Chem. Soc. 1979, 101, 1700) of the gauche effect between atoms and groups as a conformational driving force acting upon the pentofuranose ring is explored. Their model invokes maximum antiperiplanar sigma <--> sigma stabilization when the donating bond is the least polar one and the acceptor orbital is at the most polarized bond and is found at least as satisfactory, and in various specific cases more so than, as rationalizations on the basis of the preference of the gauche vs the trans conformation of two vicinal electronegative substituents (Wolfe. Acc. Chem. Res. 1972, 5, 102).